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I have been experiencing the same issue with SQL Compare 11. It does not occur with SQL Compare 10, so I am not able to upgrade until this bug has been fixed.
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There was a bug in SQL Compare 11.0 and 11.1 (our reference SC-7610) which caused the object existence checks option to generate incorrect checks, and therefore not actually update stored procedure definitions. I'm pleased to tell you that this bug has been fixed in the latest version of SQL Compare, 11.1.2.28. You can get this version via Help -> Check for Updates..., or you can download it from here (release notes).
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The options that have turned on are Object existence checks, donot use transactions.